NucMap


38878855	NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species. [PMID: 38878855] Nie Z, Zhao Y, Yu S, Mai J, Gao H, Fan Z, Bao Y, Li R, Xiao J. Abstract Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface. J Mol Biol. 2024:436(17) \| 0 Citations (from Europe PMC, 2025-03-22)
30335176	NucMap: a database of genome-wide nucleosome positioning map across species. [PMID: 30335176] Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J. Abstract Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation. Nucleic Acids Res. 2019:47(D1) \| 25 Citations (from Europe PMC, 2025-03-22)

NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species. [PMID: 38878855]

Nie Z, Zhao Y, Yu S, Mai J, Gao H, Fan Z, Bao Y, Li R, Xiao J.

Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface.

J Mol Biol. 2024:436(17) | 0 Citations (from Europe PMC, 2025-03-22)

NucMap: a database of genome-wide nucleosome positioning map across species. [PMID: 30335176]

Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J.

Abstract

Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.

Nucleic Acids Res. 2019:47(D1) | 25 Citations (from Europe PMC, 2025-03-22)

URL:	https://ngdc.cncb.ac.cn/nucmap
Full name:	Nucleosome Positioning Map
Description:	NucMap is a database of genome-wide nucleosome positioning map across species. It provides services on querying and visualizing nucleosome positioning information at single nucleotide resolution. Users can also perform enrichment analysis and comparative analysis of all collected samples.
Year founded:	2019
Last update:	2025-01-22
Version:	v2.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA
Data object:	Animal Fungi Plant
Database category:	Gene genome and annotation
Major species:	Homo sapiens Drosophila melanogaster Mus musculus Saccharomyces cerevisiae Arabidopsis thaliana
Keywords:	nucleotide nucleosome chromatin accessibility

University/Institution:	Beijing Institute of Genomics, Chinese Academy of Sciences
Address:	No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
City:	Beijing
Province/State:	Beijing
Country/Region:	China
Contact name (PI/Team):	Rujiao Li
Contact email (PI/Helpdesk):	lirj@big.ac.cn

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Database Commons a catalog of worldwide biological databases